While I still err on the side of the CCW'ers, and I'm sure much of the aquarium's reasons are "PC" ones, I can sort of see that the Aquarium also has a practical interest in banning firearms too.
I'm sure the biggest tanks, tunnels, or viewing windows, are probably polymer, and could probably stop a .50 BMG, but a bullet in one would still necessitate a multi-million dollar repair job. But I'd have to think it's also likely there's lots of "smaller" exhibit tanks that could shatter. It could still be thousands of gallons of water. Not to mention the fish...
Lockers for CCW's at the security checkpoint would be a good compromise IMO.
You're very unlikely to need your CCW in the aquarium, but from what I hear, you stand a good chance of needing it to, and from, your car.